SMTL ID : 4k4i.1 (3 other biounits)

Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)FTC-TP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x DC- DA- DG- DT- DA- DC: DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')(Non-covalent)

DC-DA-DG-DT-DA-DC.1: 23 residues within 4Å: Chain A: I.98, W.99, G.100, A.101, G.102, T.103, K.104, T.105, D.186, L.231, R.245, D.247, Y.262 Chain B: G.5, G.6, T.7, A.8, C.9, T.10, G.11 Ligands: 1RY.3, CA.4, CA.8 Protein-ligand interaction information (PLIP) not available

1 x DG- DC- DC- DG: DNA (5'-D(P*GP*CP*CP*G)-3')(Non-covalent)

DG-DC-DC-DG.2: 20 residues within 4Å: Chain A: Y.24, W.31, R.32, G.35, Y.36, I.59, P.60, G.61, I.62, G.63, K.64, R.65, M.66, K.69, K.81 Chain B: C.1, G.2, G.3, C.4 Ligands: CA.5 Protein-ligand interaction information (PLIP) not available

1 x 1RY: [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

1RY.3: 17 residues within 4Å: Chain A: R.143, G.173, S.174, R.177, C.182, G.183, D.184, D.186, Y.262, F.263, G.265, A.267, N.270 Chain B: G.5 Ligands: DC-DA-DG-DT-DA-DC.1, CA.7, CA.8 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.174, A:S.174, A:G.183, A:D.184, A:D.184, A:D.184, A:N.270 Water bridges: A:Y.175, A:Y.175, A:A.267 Salt bridges: A:R.143, A:R.177

7 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.4: 5 residues within 4Å: Chain A: S.96, I.98, G.100, A.101 Ligands: DC-DA-DG-DT-DA-DC.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.96, A:I.98, A:A.101, H2O.5, H2O.6 CA.5: 5 residues within 4Å: Chain A: C.57, I.59, P.60, I.62 Ligands: DG-DC-DC-DG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.57, A:I.59, A:I.62, H2O.5 CA.6: 2 residues within 4Å: Chain A: S.220 Chain B: T.10 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.220, H2O.3, H2O.3, H2O.4, H2O.5 CA.7: 4 residues within 4Å: Chain A: D.184, D.186 Ligands: 1RY.3, CA.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.184, A:D.184, A:D.186, H2O.1 CA.8: 6 residues within 4Å: Chain A: D.184, D.186, D.247 Ligands: DC-DA-DG-DT-DA-DC.1, 1RY.3, CA.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.184, A:D.184, A:D.186, A:D.247 CA.9: 3 residues within 4Å: Chain A: E.153, Q.157, C.169 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.153, A:C.169 CA.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 4 residues within 4Å: Chain A: A.257, L.260, T.312, E.313 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.313 Water bridges: A:T.312, A:E.313, A:K.314 ACT.12: 2 residues within 4Å: Chain B: G.2, G.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vyas, R. et al., Structural basis for the binding and incorporation of nucleotide analogs with L-stereochemistry by human DNA polymerase lambda. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-07-16

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

Related Entries With Identical Sequence